4IVY

Crystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with Dynamic WAY-derivative, 7a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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This is version 1.3 of the entry. See complete history


Literature

Ligand binding dynamics rewire cellular signaling via Estrogen Receptor-alpha

Srinivasan, S.Nwachukwu, J.C.Parent, A.A.Cavett, V.Nowak, J.Hughes, T.S.Kojetin, D.J.Katzenellenbogen, J.A.Nettles, K.W.

(2013) Nat Chem Biol 9: 326-332

  • DOI: 10.1038/nchembio.1214
  • Primary Citation of Related Structures:  
    4IU7, 4IUI, 4IV2, 4IV4, 4IVW, 4IVY, 4IW6, 4IW8, 4IWC, 4IWF

  • PubMed Abstract: 
  • Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands) ...

    Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands). Proliferation of breast cancer cells directed by constrained ligands is associated with DNA binding, coactivator recruitment and activation of the estrogen-induced gene GREB1, reflecting a highly interconnected signaling network. In contrast, proliferation driven by dynamic ligands is associated with induction of ERα-mediated transcription in a DNA-binding domain (DBD)-dependent manner. Further, dynamic ligands showed enhanced anti-inflammatory activity. The DBD-dependent profile was predictive of these signaling patterns in a larger diverse set of natural and synthetic ligands. Thus, ligand dynamics directs unique signaling pathways and reveals a new role of the DBD in allosteric control of ERα-mediated signaling.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA,
C [auth B]
247Homo sapiensMutation(s): 1 
Gene Names: ESRESR1NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
Entity Groups  
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UniProt GroupP03372
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B [auth C],
D
10Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1GT
Query on 1GT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
4-[1-(but-3-en-1-yl)-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol
C18 H15 F3 N2 O2
WNFWHTBNIWQRLE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.746α = 90
b = 81.545β = 109.87
c = 58.45γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2020-02-26
    Changes: Advisory, Database references, Derived calculations